Starting phenix.real_space_refine
on Wed Jun 11 11:05:01 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9dus_47176/06_2025/9dus_47176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dus_47176/06_2025/9dus_47176.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dus_47176/06_2025/9dus_47176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dus_47176/06_2025/9dus_47176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dus_47176/06_2025/9dus_47176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dus_47176/06_2025/9dus_47176.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    8101      2.51       5
     N    2201      2.21       5
     O    2338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12702
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 10069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1253, 10069
          Classifications: {'peptide': 1253}
          Link IDs: {'PTRANS': 52, 'TRANS': 1200}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 576
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 74, 570
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 4, 'TRANS': 69}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 74, 570
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 4, 'TRANS': 69}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 567
    Chain: "C"
      Number of atoms: 1039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1039
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 4, 'TRANS': 127}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 442
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "E"
      Number of atoms: 576
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 74, 571
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 5, 'TRANS': 68}
      Conformer: "B"
        Number of residues, atoms: 74, 571
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 5, 'TRANS': 68}
          bond proxies already assigned to first conformer: 571
  Time building chain proxies: 8.16, per 1000 atoms: 0.64
  Number of scatterers: 12702
  At special positions: 0
  Unit cell: (99.1573, 107.125, 165.557, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    2338      8.00
     N    2201      7.00
     C    8101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3012

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 7 sheets defined
      61.9% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 32
      removed outlier: 4.009A  pdb=" N   ILE A  25 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 56
      removed outlier: 4.440A  pdb=" N   LYS A  50 " --> pdb=" O   CYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 77
      removed outlier: 3.758A  pdb=" N   GLU A  67 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A  68 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 95
    Processing helix  chain 'A' and resid 103 through 135
      removed outlier: 3.584A  pdb=" N   ARG A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   ASP A 122 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   LYS A 123 " --> pdb=" O   LYS A 119 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU A 135 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 151
      removed outlier: 4.041A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 158
    Processing helix  chain 'A' and resid 161 through 183
      removed outlier: 3.696A  pdb=" N   PHE A 167 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 248
    Processing helix  chain 'A' and resid 251 through 273
      removed outlier: 3.734A  pdb=" N   GLY A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 275 through 293
      removed outlier: 4.034A  pdb=" N   ILE A 279 " --> pdb=" O   PRO A 275 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   GLU A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
      removed outlier: 4.336A  pdb=" N   LEU A 288 " --> pdb=" O   GLU A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 319
      removed outlier: 3.787A  pdb=" N   ASN A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   HIS A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN A 319 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 339
      removed outlier: 3.824A  pdb=" N   TYR A 327 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   HIS A 328 " --> pdb=" O   GLU A 324 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A 339 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 3.745A  pdb=" N   ILE A 349 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 375
      removed outlier: 4.020A  pdb=" N   ALA A 366 " --> pdb=" O   GLU A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 404
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 439
    Processing helix  chain 'A' and resid 440 through 444
      removed outlier: 3.529A  pdb=" N   PHE A 443 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 480
      removed outlier: 4.244A  pdb=" N   VAL A 479 " --> pdb=" O   TRP A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 3.523A  pdb=" N   LEU A 485 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 505
      removed outlier: 3.622A  pdb=" N   VAL A 501 " --> pdb=" O   ARG A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 519
      removed outlier: 3.904A  pdb=" N   VAL A 513 " --> pdb=" O   ASP A 509 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ILE A 514 " --> pdb=" O   PRO A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 567
    Processing helix  chain 'A' and resid 568 through 573
      removed outlier: 3.680A  pdb=" N   PHE A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS A 573 " --> pdb=" O   GLY A 569 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 568 through 573'
    Processing helix  chain 'A' and resid 666 through 671
      removed outlier: 3.682A  pdb=" N   ASN A 670 " --> pdb=" O   LYS A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 688
      removed outlier: 4.827A  pdb=" N   LEU A 678 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   PHE A 679 " --> pdb=" O   THR A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 701
      removed outlier: 3.664A  pdb=" N   LYS A 698 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 725
    Processing helix  chain 'A' and resid 743 through 763
      Proline residue:  A 753  - end of helix
    Processing helix  chain 'A' and resid 788 through 815
      removed outlier: 3.698A  pdb=" N   LYS A 792 " --> pdb=" O   PRO A 788 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS A 793 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A 794 " --> pdb=" O   ASN A 790 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 814 " --> pdb=" O   ARG A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 852
      removed outlier: 4.376A  pdb=" N   ILE A 850 " --> pdb=" O   SER A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 882
      removed outlier: 3.642A  pdb=" N   ALA A 867 " --> pdb=" O   GLU A 863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 906
    Processing helix  chain 'A' and resid 913 through 923
      removed outlier: 3.608A  pdb=" N   ILE A 918 " --> pdb=" O   ARG A 914 " (cutoff:3.500A)
      Proline residue:  A 919  - end of helix
    Processing helix  chain 'A' and resid 923 through 933
      removed outlier: 3.654A  pdb=" N   LEU A 927 " --> pdb=" O   ASN A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 938
    Processing helix  chain 'A' and resid 955 through 970
    Processing helix  chain 'A' and resid 975 through 983
      removed outlier: 3.897A  pdb=" N   HIS A 979 " --> pdb=" O   GLU A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 997
    Processing helix  chain 'A' and resid 1008 through 1024
    Processing helix  chain 'A' and resid 1027 through 1031
      removed outlier: 4.059A  pdb=" N   LYS A1031 " --> pdb=" O   PRO A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1050
      removed outlier: 3.640A  pdb=" N   GLU A1041 " --> pdb=" O   ASP A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1067
      removed outlier: 3.734A  pdb=" N   ALA A1060 " --> pdb=" O   VAL A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1079
      removed outlier: 3.695A  pdb=" N   LEU A1079 " --> pdb=" O   ILE A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1093
      removed outlier: 3.884A  pdb=" N   ILE A1086 " --> pdb=" O   THR A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1104
    Processing helix  chain 'A' and resid 1105 through 1120
    Processing helix  chain 'A' and resid 1132 through 1145
    Processing helix  chain 'A' and resid 1145 through 1150
    Processing helix  chain 'A' and resid 1161 through 1165
    Processing helix  chain 'A' and resid 1176 through 1183
      removed outlier: 3.649A  pdb=" N   CYS A1180 " --> pdb=" O   THR A1176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1249
    Processing helix  chain 'A' and resid 1252 through 1264
      removed outlier: 3.749A  pdb=" N   ASN A1257 " --> pdb=" O   ASP A1253 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLU A1258 " --> pdb=" O   SER A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1270 through 1278
    Processing helix  chain 'A' and resid 1304 through 1309
    Processing helix  chain 'A' and resid 1330 through 1348
    Processing helix  chain 'B' and resid 326 through 340
      removed outlier: 3.558A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 368
    Processing helix  chain 'B' and resid 405 through 410
    Processing helix  chain 'C' and resid 324 through 371
      removed outlier: 3.992A  pdb=" N   GLY C 344 " --> pdb=" O   LEU C 340 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLU C 345 " --> pdb=" O   LEU C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 457 through 470
      removed outlier: 4.087A  pdb=" N   ARG C 461 " --> pdb=" O   GLY C 457 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER C 462 " --> pdb=" O   PRO C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 474 through 488
    Processing helix  chain 'C' and resid 490 through 507
    Processing helix  chain 'D' and resid 325 through 369
      removed outlier: 3.834A  pdb=" N   GLY D 344 " --> pdb=" O   LEU D 340 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU D 345 " --> pdb=" O   LEU D 341 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 325 through 341
      removed outlier: 4.260A  pdb=" N   SER E 338 " --> pdb=" O   SER E 334 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU E 339 " --> pdb=" O   LYS E 335 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 341 through 374
      removed outlier: 4.040A  pdb=" N   GLU E 345 " --> pdb=" O   LEU E 341 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE E 358 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE E 372 " --> pdb=" O   SER E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 383 through 387
      removed outlier: 3.574A  pdb=" N   ASP E 387 " --> pdb=" O   PRO E 384 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.384A  pdb=" N   SER A  83 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   TYR A 222 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS A 219 " --> pdb=" O   SER A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 381
      removed outlier: 6.888A  pdb=" N   ILE B 398 " --> pdb=" O   ALA D 373 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412
      removed outlier: 3.559A  pdb=" N   LYS A 447 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549
      removed outlier: 3.958A  pdb=" N   TYR A 706 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 765 through 770
      removed outlier: 3.544A  pdb=" N   VAL A 656 " --> pdb=" O   LYS A 781 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 829 through 831
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1166 through 1171
      removed outlier: 3.657A  pdb=" N   VAL A1360 " --> pdb=" O   ILE A1171 " (cutoff:3.500A)

    708 hydrogen bonds defined for protein.
    2053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.86

  Time building geometry restraints manager: 3.03 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 4094
        1.34 -     1.46: 2065
        1.46 -     1.58: 6687
        1.58 -     1.69: 0
        1.69 -     1.81: 103
  Bond restraints: 12949
  Sorted by residual:
  bond pdb=" C   PHE A 269 "
       pdb=" N   PRO A 270 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.027 1.36e-02 5.41e+03 4.04e+00
  bond pdb=" N   ILE A 752 "
       pdb=" CA  ILE A 752 "
    ideal  model  delta    sigma   weight residual
    1.464  1.486 -0.022 1.23e-02 6.61e+03 3.18e+00
  bond pdb=" C   ILE A 918 "
       pdb=" N   PRO A 919 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.28e-02 6.10e+03 3.02e+00
  bond pdb=" C   ILE A 752 "
       pdb=" N   PRO A 753 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.28e-02 6.10e+03 3.01e+00
  bond pdb=" CA  ILE A 752 "
       pdb=" C   ILE A 752 "
    ideal  model  delta    sigma   weight residual
    1.520  1.534 -0.014 8.80e-03 1.29e+04 2.70e+00
  ... (remaining 12944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 17062
        1.98 -     3.97: 369
        3.97 -     5.95: 47
        5.95 -     7.93: 20
        7.93 -     9.91: 3
  Bond angle restraints: 17501
  Sorted by residual:
  angle pdb=" C   THR A1082 "
        pdb=" CA  THR A1082 "
        pdb=" CB  THR A1082 "
      ideal   model   delta    sigma   weight residual
     115.79  110.22    5.57 1.19e+00 7.06e-01 2.19e+01
  angle pdb=" C   LEU E 394 "
        pdb=" N   LYS E 395 "
        pdb=" CA  LYS E 395 "
      ideal   model   delta    sigma   weight residual
     121.80  131.40   -9.60 2.44e+00 1.68e-01 1.55e+01
  angle pdb=" C   ALA C 373 "
        pdb=" N   ILE C 374 "
        pdb=" CA  ILE C 374 "
      ideal   model   delta    sigma   weight residual
     122.13  128.79   -6.66 1.85e+00 2.92e-01 1.29e+01
  angle pdb=" C   GLY A 741 "
        pdb=" N   TYR A 742 "
        pdb=" CA  TYR A 742 "
      ideal   model   delta    sigma   weight residual
     121.54  128.23   -6.69 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" C   PRO E 392 "
        pdb=" N   ASP E 393 "
        pdb=" CA  ASP E 393 "
      ideal   model   delta    sigma   weight residual
     121.54  128.21   -6.67 1.91e+00 2.74e-01 1.22e+01
  ... (remaining 17496 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.99: 7240
       14.99 -    29.97: 525
       29.97 -    44.96: 119
       44.96 -    59.95: 9
       59.95 -    74.94: 7
  Dihedral angle restraints: 7900
    sinusoidal: 3248
      harmonic: 4652
  Sorted by residual:
  dihedral pdb=" CA  ILE E 390 "
           pdb=" C   ILE E 390 "
           pdb=" N   ASN E 391 "
           pdb=" CA  ASN E 391 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.22   25.78     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  HIS A1174 "
           pdb=" C   HIS A1174 "
           pdb=" N   GLU A1175 "
           pdb=" CA  GLU A1175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.57   25.43     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ILE A 766 "
           pdb=" C   ILE A 766 "
           pdb=" N   ALA A 767 "
           pdb=" CA  ALA A 767 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.14   21.86     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 7897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1880
       0.095 -    0.190: 114
       0.190 -    0.286: 5
       0.286 -    0.381: 0
       0.381 -    0.476: 1
  Chirality restraints: 2000
  Sorted by residual:
  chirality pdb=" CG  LEU A 705 "
            pdb=" CB  LEU A 705 "
            pdb=" CD1 LEU A 705 "
            pdb=" CD2 LEU A 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.67e+00
  chirality pdb=" CB  ILE E 372 "
            pdb=" CA  ILE E 372 "
            pdb=" CG1 ILE E 372 "
            pdb=" CG2 ILE E 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ASP A 466 "
            pdb=" N   ASP A 466 "
            pdb=" C   ASP A 466 "
            pdb=" CB  ASP A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.55e-01
  ... (remaining 1997 not shown)

  Planarity restraints: 2212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 274 "    0.055 5.00e-02 4.00e+02   8.15e-02 1.06e+01
        pdb=" N   PRO A 275 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 275 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 275 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 408 "   -0.016 2.00e-02 2.50e+03   2.03e-02 1.03e+01
        pdb=" CG  TRP A 408 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 408 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 408 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 408 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 408 "    0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 408 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 408 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 408 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 408 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 752 "    0.049 5.00e-02 4.00e+02   7.32e-02 8.57e+00
        pdb=" N   PRO A 753 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 753 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 753 "    0.041 5.00e-02 4.00e+02
  ... (remaining 2209 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3580
        2.83 -     3.34: 11524
        3.34 -     3.86: 20296
        3.86 -     4.38: 24016
        4.38 -     4.90: 41638
  Nonbonded interactions: 101054
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" OD1 ASP A 335 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   TRP A 747 "
            pdb=" OG1 THR A 751 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OH  TYR A 673 "
            pdb=" OE1 GLN A 694 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   LEU A1274 "
            pdb=" OG1 THR A1278 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   ALA A 796 "
            pdb=" OG1 THR A 800 "
     model   vdw
     2.365 3.040
  ... (remaining 101049 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     29.750
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  12949  Z= 0.186
  Angle     :  0.731   9.915  17501  Z= 0.402
  Chirality :  0.048   0.476   2000
  Planarity :  0.008   0.082   2212
  Dihedral  : 11.116  74.935   4888
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.18), residues: 1566
  helix: -0.60 (0.14), residues: 873
  sheet:  0.98 (0.59), residues: 80
  loop : -1.43 (0.22), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 408 
 HIS   0.008   0.001   HIS A 812 
 PHE   0.029   0.002   PHE A 304 
 TYR   0.026   0.002   TYR A 522 
 ARG   0.004   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18792 (  708)
  hydrogen bonds       : angle       6.45483 ( 2053)
  covalent geometry    : bond        0.00369 (12949)
  covalent geometry    : angle       0.73148 (17501)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7115 (mtt180)
REVERT: A   50 LYS cc_start: 0.8240 (ttmt) cc_final: 0.8002 (mtpp)
REVERT: A   62 ILE cc_start: 0.7905 (mm) cc_final: 0.7471 (mt)
REVERT: A  111 LYS cc_start: 0.7553 (ttmt) cc_final: 0.7335 (ttmm)
REVERT: A  355 SER cc_start: 0.8255 (m) cc_final: 0.7989 (p)
REVERT: A  361 LEU cc_start: 0.8234 (mt) cc_final: 0.7991 (mt)
REVERT: A  435 GLN cc_start: 0.8520 (mt0) cc_final: 0.8281 (mt0)
REVERT: A  500 ASP cc_start: 0.6941 (t0) cc_final: 0.6491 (t70)
REVERT: A  516 TYR cc_start: 0.8101 (t80) cc_final: 0.7788 (t80)
REVERT: A  533 SER cc_start: 0.7921 (t) cc_final: 0.7495 (p)
REVERT: A  535 LYS cc_start: 0.8135 (tppt) cc_final: 0.7927 (mmtp)
REVERT: A  546 PHE cc_start: 0.7164 (p90) cc_final: 0.6677 (p90)
REVERT: A  559 ILE cc_start: 0.8339 (mt) cc_final: 0.7932 (mt)
REVERT: A  563 LEU cc_start: 0.7655 (mt) cc_final: 0.7399 (mp)
REVERT: A  570 LYS cc_start: 0.8022 (mttt) cc_final: 0.7769 (mttt)
REVERT: A  573 LYS cc_start: 0.7532 (mtpp) cc_final: 0.7324 (mtpp)
REVERT: A  861 VAL cc_start: 0.7413 (t) cc_final: 0.7136 (m)
REVERT: A  923 ASN cc_start: 0.8299 (t0) cc_final: 0.7986 (t0)
REVERT: A  925 ASP cc_start: 0.7296 (m-30) cc_final: 0.7015 (m-30)
REVERT: A 1019 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7337 (mtp85)
REVERT: A 1090 MET cc_start: 0.7006 (ttt) cc_final: 0.6648 (ttt)
REVERT: A 1144 MET cc_start: 0.8124 (mmm) cc_final: 0.7841 (mmm)
REVERT: A 1240 ARG cc_start: 0.7386 (tpt170) cc_final: 0.7169 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7286 (mttt) cc_final: 0.7011 (mttt)
REVERT: C  371 MET cc_start: 0.6812 (ptp) cc_final: 0.6579 (ptp)
REVERT: C  460 SER cc_start: 0.7749 (p) cc_final: 0.7450 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.2802
  time to fit residues: 118.0812
Evaluate side-chains
  258 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:   10.0000
   chunk 118 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 40 optimal weight:    0.2980
   chunk 80 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 123 optimal weight:    0.0030
   chunk 47 optimal weight:    0.4980
   chunk 74 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0060
   chunk 142 optimal weight:    0.5980
   overall best weight:    0.2806

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 HIS
A 809 GLN
B 329 ASN
C 356 GLN
E 329 ASN
E 356 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.153852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.121787 restraints weight = 36873.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 3.49
r_work: 0.3260 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12949  Z= 0.131
  Angle     :  0.514   7.363  17501  Z= 0.278
  Chirality :  0.039   0.144   2000
  Planarity :  0.005   0.050   2212
  Dihedral  :  4.308  23.955   1735
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  6.27 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.20), residues: 1566
  helix:  1.52 (0.17), residues: 887
  sheet:  1.28 (0.55), residues: 97
  loop : -1.16 (0.23), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1189 
 HIS   0.011   0.001   HIS A 157 
 PHE   0.019   0.002   PHE A 392 
 TYR   0.019   0.001   TYR A 789 
 ARG   0.007   0.000   ARG A  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05866 (  708)
  hydrogen bonds       : angle       4.37996 ( 2053)
  covalent geometry    : bond        0.00265 (12949)
  covalent geometry    : angle       0.51421 (17501)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 271
  time to evaluate  : 1.321 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7524 (mtt90) cc_final: 0.7271 (mtt-85)
REVERT: A   50 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8123 (mtpp)
REVERT: A   77 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7680 (ttm-80)
REVERT: A  264 LEU cc_start: 0.8202 (tp) cc_final: 0.8000 (tp)
REVERT: A  355 SER cc_start: 0.8467 (m) cc_final: 0.8231 (p)
REVERT: A  361 LEU cc_start: 0.8291 (mt) cc_final: 0.8069 (mt)
REVERT: A  500 ASP cc_start: 0.6945 (t0) cc_final: 0.6568 (t70)
REVERT: A  516 TYR cc_start: 0.8093 (t80) cc_final: 0.7839 (t80)
REVERT: A  535 LYS cc_start: 0.8180 (tppt) cc_final: 0.7923 (mmtp)
REVERT: A  570 LYS cc_start: 0.8165 (mttt) cc_final: 0.7895 (mttt)
REVERT: A  573 LYS cc_start: 0.7569 (mtpp) cc_final: 0.7352 (mtpp)
REVERT: A  752 ILE cc_start: 0.8544 (mt) cc_final: 0.8279 (mp)
REVERT: A  780 THR cc_start: 0.7938 (m) cc_final: 0.7661 (p)
REVERT: A  803 TYR cc_start: 0.8184 (t80) cc_final: 0.7951 (t80)
REVERT: A  861 VAL cc_start: 0.7489 (t) cc_final: 0.7186 (m)
REVERT: A  923 ASN cc_start: 0.8364 (t0) cc_final: 0.7943 (t0)
REVERT: A  925 ASP cc_start: 0.7321 (m-30) cc_final: 0.7065 (m-30)
REVERT: A  930 MET cc_start: 0.7862 (ttp) cc_final: 0.7605 (ttp)
REVERT: A  969 LEU cc_start: 0.8397 (tp) cc_final: 0.8173 (tt)
REVERT: A 1062 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7253 (mm-30)
REVERT: A 1090 MET cc_start: 0.7094 (ttt) cc_final: 0.6759 (ttt)
REVERT: A 1112 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7465 (ttm-80)
REVERT: A 1144 MET cc_start: 0.8199 (mmm) cc_final: 0.7835 (mmm)
REVERT: A 1150 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7300 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7476 (tpt170) cc_final: 0.7164 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7331 (mttt) cc_final: 0.7047 (mttt)
REVERT: C  446 MET cc_start: 0.5994 (mmt) cc_final: 0.5772 (mmt)
REVERT: C  460 SER cc_start: 0.7799 (p) cc_final: 0.7513 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 272
  average time/residue: 0.2780
  time to fit residues: 105.0994
Evaluate side-chains
  269 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 264
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain E residue  371 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 144 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 125 optimal weight:    5.9990
   chunk 108 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 147 optimal weight:    3.9990
   chunk 116 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 504 ASN
A 809 GLN
A1186 ASN
C 356 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.149155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.116868 restraints weight = 34602.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 3.42
r_work: 0.3192 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12949  Z= 0.196
  Angle     :  0.567   6.419  17501  Z= 0.303
  Chirality :  0.042   0.153   2000
  Planarity :  0.005   0.044   2212
  Dihedral  :  4.414  23.519   1735
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  6.83 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.21), residues: 1566
  helix:  1.82 (0.17), residues: 898
  sheet:  1.04 (0.53), residues: 96
  loop : -1.20 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 408 
 HIS   0.013   0.001   HIS A 157 
 PHE   0.025   0.002   PHE A 304 
 TYR   0.025   0.002   TYR A 516 
 ARG   0.005   0.000   ARG A 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06286 (  708)
  hydrogen bonds       : angle       4.35851 ( 2053)
  covalent geometry    : bond        0.00453 (12949)
  covalent geometry    : angle       0.56731 (17501)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 269
  time to evaluate  : 1.398 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7398 (mtt180)
REVERT: A   50 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8240 (mtpp)
REVERT: A   77 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7781 (ttm-80)
REVERT: A  250 ARG cc_start: 0.8312 (ttp-170) cc_final: 0.8089 (ttp80)
REVERT: A  435 GLN cc_start: 0.8415 (mt0) cc_final: 0.8170 (mt0)
REVERT: A  570 LYS cc_start: 0.8141 (mttt) cc_final: 0.7729 (mttt)
REVERT: A  573 LYS cc_start: 0.7489 (mtpp) cc_final: 0.7260 (mtpp)
REVERT: A  780 THR cc_start: 0.7969 (m) cc_final: 0.7683 (p)
REVERT: A  803 TYR cc_start: 0.8281 (t80) cc_final: 0.7881 (t80)
REVERT: A  861 VAL cc_start: 0.7707 (t) cc_final: 0.7413 (m)
REVERT: A  923 ASN cc_start: 0.8350 (t0) cc_final: 0.7920 (t0)
REVERT: A  925 ASP cc_start: 0.7366 (m-30) cc_final: 0.7133 (m-30)
REVERT: A  930 MET cc_start: 0.7917 (ttp) cc_final: 0.7689 (ttp)
REVERT: A 1019 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7408 (mtp85)
REVERT: A 1090 MET cc_start: 0.7044 (ttt) cc_final: 0.6745 (ttt)
REVERT: A 1108 TYR cc_start: 0.7807 (t80) cc_final: 0.7431 (t80)
REVERT: A 1110 GLN cc_start: 0.7292 (mt0) cc_final: 0.6986 (mt0)
REVERT: A 1112 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7444 (ttm-80)
REVERT: A 1150 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7275 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7515 (tpt170) cc_final: 0.7173 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7573 (mttt) cc_final: 0.7268 (mttt)
REVERT: C  446 MET cc_start: 0.5949 (mmt) cc_final: 0.5745 (mmt)
REVERT: C  460 SER cc_start: 0.7813 (p) cc_final: 0.7572 (m)
  outliers start: 21
  outliers final: 18
  residues processed: 274
  average time/residue: 0.3013
  time to fit residues: 113.3792
Evaluate side-chains
  278 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 260
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue 1132 CYS
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 145 optimal weight:    4.9990
   chunk 123 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 85 optimal weight:    0.3980
   chunk 117 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 809 GLN
A 812 HIS
A1186 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.149666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.116335 restraints weight = 41590.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.82
r_work: 0.3169 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12949  Z= 0.158
  Angle     :  0.522   7.099  17501  Z= 0.276
  Chirality :  0.040   0.154   2000
  Planarity :  0.004   0.043   2212
  Dihedral  :  4.286  23.282   1735
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  8.73 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.21), residues: 1566
  helix:  2.14 (0.17), residues: 890
  sheet:  0.89 (0.52), residues: 96
  loop : -1.22 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 408 
 HIS   0.012   0.001   HIS A 157 
 PHE   0.022   0.002   PHE A 546 
 TYR   0.019   0.002   TYR A 516 
 ARG   0.008   0.000   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05604 (  708)
  hydrogen bonds       : angle       4.23571 ( 2053)
  covalent geometry    : bond        0.00360 (12949)
  covalent geometry    : angle       0.52243 (17501)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 268
  time to evaluate  : 2.146 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7338 (mtt-85)
REVERT: A   50 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8283 (mtpp)
REVERT: A  250 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.8095 (ttp80)
REVERT: A  435 GLN cc_start: 0.8443 (mt0) cc_final: 0.8184 (mt0)
REVERT: A  522 TYR cc_start: 0.8245 (p90) cc_final: 0.7817 (p90)
REVERT: A  535 LYS cc_start: 0.8225 (mmtp) cc_final: 0.8023 (mmtp)
REVERT: A  570 LYS cc_start: 0.8123 (mttt) cc_final: 0.7901 (mttt)
REVERT: A  573 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7317 (mtpp)
REVERT: A  780 THR cc_start: 0.7970 (m) cc_final: 0.7711 (p)
REVERT: A  803 TYR cc_start: 0.8239 (t80) cc_final: 0.7905 (t80)
REVERT: A  861 VAL cc_start: 0.7721 (t) cc_final: 0.7435 (m)
REVERT: A  923 ASN cc_start: 0.8370 (t0) cc_final: 0.7926 (t0)
REVERT: A  925 ASP cc_start: 0.7373 (m-30) cc_final: 0.7143 (m-30)
REVERT: A  930 MET cc_start: 0.7965 (ttp) cc_final: 0.7743 (ttp)
REVERT: A  969 LEU cc_start: 0.8250 (tt) cc_final: 0.8044 (tt)
REVERT: A 1019 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7486 (mtp85)
REVERT: A 1090 MET cc_start: 0.7047 (ttt) cc_final: 0.6746 (ttt)
REVERT: A 1110 GLN cc_start: 0.7290 (mt0) cc_final: 0.7000 (mt0)
REVERT: A 1150 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7288 (mtp-110)
REVERT: A 1240 ARG cc_start: 0.7585 (tpt170) cc_final: 0.7231 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7599 (mttt) cc_final: 0.7295 (mttt)
REVERT: C  446 MET cc_start: 0.5994 (mmt) cc_final: 0.5779 (mmt)
REVERT: C  460 SER cc_start: 0.7831 (p) cc_final: 0.7588 (m)
  outliers start: 24
  outliers final: 20
  residues processed: 276
  average time/residue: 0.3597
  time to fit residues: 137.2029
Evaluate side-chains
  284 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 264
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue 1132 CYS
Chi-restraints excluded: chain A residue 1186 ASN
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 GLN
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 809 GLN
A 812 HIS
A1053 HIS
** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.149234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.117642 restraints weight = 25928.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.58
r_work: 0.3280 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12949  Z= 0.179
  Angle     :  0.537   6.575  17501  Z= 0.283
  Chirality :  0.041   0.153   2000
  Planarity :  0.004   0.038   2212
  Dihedral  :  4.313  23.193   1735
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.72 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.21), residues: 1566
  helix:  2.14 (0.17), residues: 892
  sheet:  0.74 (0.52), residues: 96
  loop : -1.27 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 408 
 HIS   0.012   0.001   HIS A 157 
 PHE   0.017   0.002   PHE A1191 
 TYR   0.020   0.002   TYR A 516 
 ARG   0.006   0.000   ARG A1147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05716 (  708)
  hydrogen bonds       : angle       4.24780 ( 2053)
  covalent geometry    : bond        0.00418 (12949)
  covalent geometry    : angle       0.53663 (17501)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 270
  time to evaluate  : 1.572 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8130 (mtpp)
REVERT: A  250 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.8021 (ttp80)
REVERT: A  435 GLN cc_start: 0.8363 (mt0) cc_final: 0.8116 (mt0)
REVERT: A  570 LYS cc_start: 0.8042 (mttt) cc_final: 0.7818 (mttt)
REVERT: A  573 LYS cc_start: 0.7467 (mtpp) cc_final: 0.7211 (mtpp)
REVERT: A  780 THR cc_start: 0.7883 (m) cc_final: 0.7594 (p)
REVERT: A  803 TYR cc_start: 0.8198 (t80) cc_final: 0.7854 (t80)
REVERT: A  861 VAL cc_start: 0.7700 (t) cc_final: 0.7426 (m)
REVERT: A  923 ASN cc_start: 0.8360 (t0) cc_final: 0.7892 (t0)
REVERT: A  925 ASP cc_start: 0.7162 (m-30) cc_final: 0.6953 (m-30)
REVERT: A  930 MET cc_start: 0.7857 (ttp) cc_final: 0.7629 (ttp)
REVERT: A 1012 LEU cc_start: 0.7888 (mt) cc_final: 0.7654 (mm)
REVERT: A 1019 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7255 (mtp85)
REVERT: A 1090 MET cc_start: 0.6828 (ttt) cc_final: 0.6569 (ttt)
REVERT: A 1110 GLN cc_start: 0.7105 (mt0) cc_final: 0.6802 (mt0)
REVERT: A 1150 ARG cc_start: 0.7303 (mtm110) cc_final: 0.7066 (mtp-110)
REVERT: A 1240 ARG cc_start: 0.7347 (tpt170) cc_final: 0.6999 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7561 (mttt) cc_final: 0.7203 (mttt)
REVERT: C  460 SER cc_start: 0.7617 (p) cc_final: 0.7390 (m)
  outliers start: 24
  outliers final: 22
  residues processed: 279
  average time/residue: 0.4087
  time to fit residues: 159.9109
Evaluate side-chains
  289 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 267
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0970
   chunk 77 optimal weight:    0.0770
   chunk 0 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 132 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 120 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4336

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 681 GLN
A 809 GLN
A 812 HIS
A1053 HIS
** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.154487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.121036 restraints weight = 44138.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 3.93
r_work: 0.3191 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12949  Z= 0.140
  Angle     :  0.505   7.369  17501  Z= 0.268
  Chirality :  0.040   0.152   2000
  Planarity :  0.004   0.037   2212
  Dihedral  :  4.204  22.881   1735
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.56 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.21), residues: 1566
  helix:  2.31 (0.17), residues: 892
  sheet:  0.74 (0.52), residues: 96
  loop : -1.28 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1189 
 HIS   0.011   0.001   HIS A 157 
 PHE   0.024   0.002   PHE A 546 
 TYR   0.018   0.001   TYR A 516 
 ARG   0.009   0.000   ARG A1112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05231 (  708)
  hydrogen bonds       : angle       4.14693 ( 2053)
  covalent geometry    : bond        0.00312 (12949)
  covalent geometry    : angle       0.50533 (17501)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 272
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8291 (mtpp)
REVERT: A  194 VAL cc_start: 0.8429 (m) cc_final: 0.8157 (t)
REVERT: A  250 ARG cc_start: 0.8332 (ttp-170) cc_final: 0.8098 (ttp80)
REVERT: A  258 VAL cc_start: 0.7960 (p) cc_final: 0.7644 (t)
REVERT: A  329 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7352 (mt-10)
REVERT: A  435 GLN cc_start: 0.8434 (mt0) cc_final: 0.8204 (mt0)
REVERT: A  570 LYS cc_start: 0.8180 (mttt) cc_final: 0.7930 (mttt)
REVERT: A  573 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7282 (mtpp)
REVERT: A  803 TYR cc_start: 0.8221 (t80) cc_final: 0.7882 (t80)
REVERT: A  861 VAL cc_start: 0.7710 (t) cc_final: 0.7431 (m)
REVERT: A  923 ASN cc_start: 0.8333 (t0) cc_final: 0.7863 (t0)
REVERT: A  925 ASP cc_start: 0.7308 (m-30) cc_final: 0.7091 (m-30)
REVERT: A  930 MET cc_start: 0.7989 (ttp) cc_final: 0.7763 (ttp)
REVERT: A 1012 LEU cc_start: 0.7945 (mt) cc_final: 0.7682 (mm)
REVERT: A 1090 MET cc_start: 0.7020 (ttt) cc_final: 0.6699 (ttt)
REVERT: A 1110 GLN cc_start: 0.7248 (mt0) cc_final: 0.6892 (mt0)
REVERT: A 1112 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7404 (ttm-80)
REVERT: A 1150 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7231 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7473 (tpt170) cc_final: 0.7097 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7621 (mttt) cc_final: 0.7248 (mttt)
REVERT: C  460 SER cc_start: 0.7662 (p) cc_final: 0.7422 (m)
  outliers start: 25
  outliers final: 20
  residues processed: 281
  average time/residue: 0.3366
  time to fit residues: 130.1906
Evaluate side-chains
  288 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 268
  time to evaluate  : 1.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9980
   chunk 130 optimal weight:    0.0370
   chunk 121 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 59 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.4458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 681 GLN
A 809 GLN
A 812 HIS
A1053 HIS
** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.154496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121366 restraints weight = 41871.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 3.85
r_work: 0.3188 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12949  Z= 0.142
  Angle     :  0.504   7.279  17501  Z= 0.267
  Chirality :  0.040   0.152   2000
  Planarity :  0.004   0.036   2212
  Dihedral  :  4.163  22.610   1735
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.85 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.21), residues: 1566
  helix:  2.38 (0.17), residues: 892
  sheet:  0.71 (0.53), residues: 96
  loop : -1.28 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1189 
 HIS   0.010   0.001   HIS A 157 
 PHE   0.017   0.001   PHE A 392 
 TYR   0.017   0.001   TYR A 516 
 ARG   0.007   0.000   ARG A1112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05130 (  708)
  hydrogen bonds       : angle       4.11442 ( 2053)
  covalent geometry    : bond        0.00318 (12949)
  covalent geometry    : angle       0.50385 (17501)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 270
  time to evaluate  : 2.722 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8299 (mtpp)
REVERT: A  194 VAL cc_start: 0.8424 (m) cc_final: 0.8162 (t)
REVERT: A  250 ARG cc_start: 0.8307 (ttp-170) cc_final: 0.8065 (ttp80)
REVERT: A  258 VAL cc_start: 0.7969 (p) cc_final: 0.7625 (t)
REVERT: A  329 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7340 (mt-10)
REVERT: A  435 GLN cc_start: 0.8430 (mt0) cc_final: 0.8201 (mt0)
REVERT: A  570 LYS cc_start: 0.8182 (mttt) cc_final: 0.7932 (mttt)
REVERT: A  573 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7285 (mtpp)
REVERT: A  681 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6717 (tm130)
REVERT: A  780 THR cc_start: 0.7965 (m) cc_final: 0.7682 (p)
REVERT: A  803 TYR cc_start: 0.8223 (t80) cc_final: 0.7879 (t80)
REVERT: A  861 VAL cc_start: 0.7714 (t) cc_final: 0.7449 (m)
REVERT: A  923 ASN cc_start: 0.8333 (t0) cc_final: 0.7834 (t0)
REVERT: A  925 ASP cc_start: 0.7314 (m-30) cc_final: 0.7099 (m-30)
REVERT: A  930 MET cc_start: 0.7995 (ttp) cc_final: 0.7776 (ttp)
REVERT: A 1012 LEU cc_start: 0.7936 (mt) cc_final: 0.7670 (mm)
REVERT: A 1090 MET cc_start: 0.7022 (ttt) cc_final: 0.6713 (ttt)
REVERT: A 1110 GLN cc_start: 0.7239 (mt0) cc_final: 0.6968 (mt0)
REVERT: A 1112 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7536 (ttp80)
REVERT: A 1150 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7268 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7485 (tpt170) cc_final: 0.7104 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7685 (mttt) cc_final: 0.7326 (mttt)
REVERT: C  460 SER cc_start: 0.7695 (p) cc_final: 0.7455 (m)
REVERT: D  366 HIS cc_start: 0.8011 (m-70) cc_final: 0.7714 (m-70)
REVERT: E  385 THR cc_start: 0.7767 (m) cc_final: 0.7331 (m)
  outliers start: 29
  outliers final: 25
  residues processed: 282
  average time/residue: 0.4852
  time to fit residues: 195.6876
Evaluate side-chains
  292 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 266
  time to evaluate  : 1.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1107 ASP
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  462 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 71 optimal weight:    0.1980
   chunk 3 optimal weight:    0.5980
   chunk 155 optimal weight:    0.7980
   chunk 116 optimal weight:    0.1980
   chunk 149 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 59 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 129 optimal weight:    4.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 681 GLN
A 812 HIS
** A1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.154473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121201 restraints weight = 34676.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 3.61
r_work: 0.3240 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3246
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12949  Z= 0.140
  Angle     :  0.509   8.608  17501  Z= 0.267
  Chirality :  0.040   0.154   2000
  Planarity :  0.004   0.033   2212
  Dihedral  :  4.130  22.377   1735
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.48 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.21), residues: 1566
  helix:  2.42 (0.17), residues: 893
  sheet:  0.57 (0.53), residues: 98
  loop : -1.27 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1189 
 HIS   0.012   0.001   HIS A 157 
 PHE   0.026   0.002   PHE A 546 
 TYR   0.017   0.001   TYR A 516 
 ARG   0.006   0.000   ARG A1112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05034 (  708)
  hydrogen bonds       : angle       4.09162 ( 2053)
  covalent geometry    : bond        0.00315 (12949)
  covalent geometry    : angle       0.50874 (17501)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 267
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8226 (mtpp)
REVERT: A  194 VAL cc_start: 0.8409 (m) cc_final: 0.8172 (t)
REVERT: A  250 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.8034 (ttp80)
REVERT: A  258 VAL cc_start: 0.7947 (p) cc_final: 0.7584 (t)
REVERT: A  329 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7271 (mt-10)
REVERT: A  435 GLN cc_start: 0.8405 (mt0) cc_final: 0.8178 (mt0)
REVERT: A  570 LYS cc_start: 0.8112 (mttt) cc_final: 0.7872 (mttt)
REVERT: A  573 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7247 (mtpp)
REVERT: A  681 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.6645 (tm130)
REVERT: A  780 THR cc_start: 0.7886 (m) cc_final: 0.7612 (p)
REVERT: A  803 TYR cc_start: 0.8228 (t80) cc_final: 0.7931 (t80)
REVERT: A  861 VAL cc_start: 0.7720 (t) cc_final: 0.7464 (m)
REVERT: A  923 ASN cc_start: 0.8351 (t0) cc_final: 0.7870 (t0)
REVERT: A  925 ASP cc_start: 0.7208 (m-30) cc_final: 0.7005 (m-30)
REVERT: A  930 MET cc_start: 0.7934 (ttp) cc_final: 0.7712 (ttp)
REVERT: A 1012 LEU cc_start: 0.7906 (mt) cc_final: 0.7648 (mm)
REVERT: A 1090 MET cc_start: 0.6932 (ttt) cc_final: 0.6642 (ttt)
REVERT: A 1110 GLN cc_start: 0.7144 (mt0) cc_final: 0.6873 (mt0)
REVERT: A 1112 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7453 (ttp80)
REVERT: A 1150 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7197 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7427 (tpt170) cc_final: 0.7061 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7690 (mttt) cc_final: 0.7322 (mttt)
REVERT: A 1392 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7205 (mt)
REVERT: D  366 HIS cc_start: 0.8018 (m-70) cc_final: 0.7707 (m-70)
REVERT: E  385 THR cc_start: 0.7781 (m) cc_final: 0.7366 (m)
  outliers start: 24
  outliers final: 20
  residues processed: 276
  average time/residue: 0.3695
  time to fit residues: 140.9141
Evaluate side-chains
  286 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 264
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ASP
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  730 ILE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue 1107 ASP
Chi-restraints excluded: chain A residue 1312 THR
Chi-restraints excluded: chain A residue 1392 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 100 optimal weight:    0.3980
   chunk 112 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0470
   chunk 63 optimal weight:    0.0040
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0040
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.2502

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 681 GLN
A 809 GLN
A1053 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.155522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.121864 restraints weight = 38410.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 3.73
r_work: 0.3235 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12949  Z= 0.113
  Angle     :  0.491   9.152  17501  Z= 0.257
  Chirality :  0.038   0.150   2000
  Planarity :  0.004   0.033   2212
  Dihedral  :  4.017  21.876   1735
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.11 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.22), residues: 1566
  helix:  2.59 (0.17), residues: 892
  sheet:  0.66 (0.53), residues: 98
  loop : -1.21 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1189 
 HIS   0.012   0.001   HIS A 157 
 PHE   0.017   0.001   PHE A 392 
 TYR   0.014   0.001   TYR A1310 
 ARG   0.006   0.000   ARG A1112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04596 (  708)
  hydrogen bonds       : angle       3.99515 ( 2053)
  covalent geometry    : bond        0.00240 (12949)
  covalent geometry    : angle       0.49074 (17501)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 264
  time to evaluate  : 1.323 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8230 (mtpp)
REVERT: A  126 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7504 (tp-100)
REVERT: A  250 ARG cc_start: 0.8250 (ttp-170) cc_final: 0.8005 (ttp80)
REVERT: A  329 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7237 (mt-10)
REVERT: A  356 PHE cc_start: 0.8513 (m-80) cc_final: 0.8152 (m-80)
REVERT: A  435 GLN cc_start: 0.8409 (mt0) cc_final: 0.8181 (mt0)
REVERT: A  570 LYS cc_start: 0.8139 (mttt) cc_final: 0.7884 (mttt)
REVERT: A  573 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7229 (mtpp)
REVERT: A  681 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.6787 (tm130)
REVERT: A  780 THR cc_start: 0.7919 (m) cc_final: 0.7627 (p)
REVERT: A  803 TYR cc_start: 0.8254 (t80) cc_final: 0.7948 (t80)
REVERT: A  861 VAL cc_start: 0.7659 (t) cc_final: 0.7404 (m)
REVERT: A  923 ASN cc_start: 0.8336 (t0) cc_final: 0.7858 (t0)
REVERT: A  925 ASP cc_start: 0.7230 (m-30) cc_final: 0.7008 (m-30)
REVERT: A  930 MET cc_start: 0.7956 (ttp) cc_final: 0.7725 (ttp)
REVERT: A 1090 MET cc_start: 0.6998 (ttt) cc_final: 0.6679 (ttt)
REVERT: A 1110 GLN cc_start: 0.7146 (mt0) cc_final: 0.6795 (mt0)
REVERT: A 1112 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7387 (ttm-80)
REVERT: A 1150 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7164 (mtp-110)
REVERT: A 1240 ARG cc_start: 0.7384 (tpt170) cc_final: 0.7014 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7629 (mttt) cc_final: 0.7264 (mttt)
REVERT: E  385 THR cc_start: 0.7746 (m) cc_final: 0.7348 (m)
  outliers start: 20
  outliers final: 16
  residues processed: 270
  average time/residue: 0.2953
  time to fit residues: 110.0239
Evaluate side-chains
  277 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 260
  time to evaluate  : 1.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1107 ASP
Chi-restraints excluded: chain A residue 1392 LEU
Chi-restraints excluded: chain C residue  448 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 142 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 141 optimal weight:    0.4980
   chunk 123 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    0.1980
   chunk 89 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 681 GLN
A1053 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.154650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.121146 restraints weight = 34574.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 3.46
r_work: 0.3245 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3251
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3251
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12949  Z= 0.148
  Angle     :  0.514   8.801  17501  Z= 0.269
  Chirality :  0.040   0.150   2000
  Planarity :  0.004   0.033   2212
  Dihedral  :  4.062  21.818   1735
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.46 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.22), residues: 1566
  helix:  2.52 (0.17), residues: 892
  sheet:  0.64 (0.54), residues: 98
  loop : -1.21 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1189 
 HIS   0.011   0.001   HIS A 157 
 PHE   0.026   0.002   PHE A 546 
 TYR   0.017   0.002   TYR A 516 
 ARG   0.006   0.000   ARG A1112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04915 (  708)
  hydrogen bonds       : angle       4.04218 ( 2053)
  covalent geometry    : bond        0.00341 (12949)
  covalent geometry    : angle       0.51435 (17501)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3132 Ramachandran restraints generated.
    1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 263
  time to evaluate  : 1.322 
Fit side-chains
REVERT: A   50 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8204 (mtpp)
REVERT: A  126 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7424 (tp-100)
REVERT: A  157 HIS cc_start: 0.8300 (m-70) cc_final: 0.7991 (m90)
REVERT: A  194 VAL cc_start: 0.8397 (m) cc_final: 0.8155 (t)
REVERT: A  250 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.8020 (ttp80)
REVERT: A  329 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7234 (mt-10)
REVERT: A  435 GLN cc_start: 0.8395 (mt0) cc_final: 0.8163 (mt0)
REVERT: A  570 LYS cc_start: 0.8113 (mttt) cc_final: 0.7865 (mttt)
REVERT: A  573 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7215 (mtpp)
REVERT: A  780 THR cc_start: 0.7875 (m) cc_final: 0.7593 (p)
REVERT: A  803 TYR cc_start: 0.8264 (t80) cc_final: 0.7970 (t80)
REVERT: A  861 VAL cc_start: 0.7690 (t) cc_final: 0.7435 (m)
REVERT: A  930 MET cc_start: 0.7916 (ttp) cc_final: 0.7700 (ttp)
REVERT: A 1012 LEU cc_start: 0.7881 (mt) cc_final: 0.7613 (mm)
REVERT: A 1090 MET cc_start: 0.6934 (ttt) cc_final: 0.6633 (ttt)
REVERT: A 1110 GLN cc_start: 0.7131 (mt0) cc_final: 0.6853 (mt0)
REVERT: A 1112 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.7346 (ttm-80)
REVERT: A 1135 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7000 (tm-30)
REVERT: A 1150 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7187 (mtp180)
REVERT: A 1240 ARG cc_start: 0.7395 (tpt170) cc_final: 0.7026 (mmm160)
REVERT: A 1352 LYS cc_start: 0.7671 (mttt) cc_final: 0.7293 (mttt)
REVERT: A 1392 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7167 (mt)
  outliers start: 19
  outliers final: 17
  residues processed: 271
  average time/residue: 0.2914
  time to fit residues: 109.0550
Evaluate side-chains
  280 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 262
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  501 VAL
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1107 ASP
Chi-restraints excluded: chain A residue 1236 ARG
Chi-restraints excluded: chain A residue 1392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 103 optimal weight:    0.5980
   chunk 138 optimal weight:    2.9990
   chunk 112 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 105 optimal weight:    0.6980
   chunk 60 optimal weight:    0.1980
   chunk 121 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
A 557 GLN
A 681 GLN
A 809 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.154154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.120155 restraints weight = 48853.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 4.36
r_work: 0.3158 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12949  Z= 0.158
  Angle     :  0.526   8.655  17501  Z= 0.274
  Chirality :  0.040   0.152   2000
  Planarity :  0.004   0.034   2212
  Dihedral  :  4.112  21.776   1735
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.54 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.21), residues: 1566
  helix:  2.47 (0.17), residues: 891
  sheet:  0.58 (0.53), residues: 98
  loop : -1.26 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 408 
 HIS   0.011   0.001   HIS A 157 
 PHE   0.018   0.002   PHE A 392 
 TYR   0.018   0.002   TYR A 516 
 ARG   0.006   0.000   ARG A1112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05084 (  708)
  hydrogen bonds       : angle       4.07641 ( 2053)
  covalent geometry    : bond        0.00370 (12949)
  covalent geometry    : angle       0.52572 (17501)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8230.78 seconds
wall clock time: 145 minutes 3.84 seconds (8703.84 seconds total)